A Soul of Silver and a Heart of Gold
by Darrith
Summary: Watch as Lyra begins her new journey into the world of Pokémon, as she encounters old friends and new enemies, and fights to defeat the Neo-Team Rocket. Join her as she fights to defeat gym leaders, hoping for a shot at the renowned champion, Lance. But what will happen when she faces one of Rock most powerful Team Rocket trainers ever? And what is up with that mask of his?
1. Chapter 1

_Disclaimer: The day I own Pokémon is the day I change the plot. As such I am not the owner of Pokémon._

Chapter 1: Lyra

Lyra walked along the road, skipping happily. It was not because of any particular reason, she was just happy as a person. Anyone in New Bark town, her hometown, would have told you that. Her motto was that she had no reason not to be happy, despite living alone with her mother.

As she skipped home she noticed her mother, a middle-aged, well off woman, talking on her pokegear.

"Hi mom!" Lyra said, coming to a stop in front of her mother who was just now putting her phone away.

"Rosa, its good that you got here so quickly!" Her mother said. "I just got a call from an old friend. Tell me, do you remember professor Elm?"

"Wasn't he the one who gave Jackson his Larvitar?"

Jackson was one of Rosa's oldest friends, being only a year older, but he had left on his own journey, about two years ago. She hadn't heard from him all that time. Lyra had another friend, Ethan, who never left New Bark, mostly because she was here, and he was waiting for her to get a pokemon so he could be her rival. He too had a pokemon, but he had raised it from an Azurill.

"That's the one." Her mother replied, snapping Lyra back to reality.

"What about him?"

"He recently just moved here." Her mother replied "And he wants to talk to you! HE lives next door in the new lab."

"OK!" Lyra said, with a smile. Was she finally going to get a pokemon of her own?  
Turning, she skipped back towards the new lab, which was about twenty feet away. Soon she was looking up at the double-decker house. Opening the door she peeked inside.

"Hello? Anyone home?" She called out.

"Oh, hello!" A middle-aged man suddenly appeared in front of her, wearing a labcoat and glasses, and sticking out a hand to shake. "You must be Lyra. I'm professor Elm."

Accepting the hand, she was soon following him to the back of the laboratory, where there was a small station with three pokeballs on it, each marked with a different insignia, which she assumed marked the balls content's type. One for fire, one for water, and one for grass. Her hope for a pokemon went up again.

"Lyra, do you know anything about my research?" Elm asked, speaking incredibly fast. "As you know, these days, pokemon are carried in pokeballs, but before those, people walked with their pokemon."

"Yup. I found that out in history class at school." Lyra replied, wondering whether or not this meant she would get a pokemon. "Ethan walks with his Marill too."

"Good. I would like to experiment with this." Elm said, confusing Lyra. "I want you to take one of these pokemon and-"

Elm was interrupted by a nearby pokegear suddenly ringing, and Elm walked over to pick it up.

"Hello? Oh Oak, what is it?" Elm asked, talking into the pokegear. "A new discovery? I'm busy, but I think I have another way."

As he finished the last sentence he looked towards Lyra, before placing the pokegear down, and walking over to her.

"Lyra, have you heard of Professor Oak?" Elm asked. "He's quite renowned as a Pokemon Professor. He just called me and told me he had found a new discovery, but I'm busy at the moment. Could I ask a favor of you?"

"Sure, what do you need done." Lyra asked, dawning a smile in hopes of recieving a pokemon.

"I need you to take one of these pokemon over to professor Oak and retrieve a package he has for me." Elm said, gesturing to the nearby machine. "Please keep the pokemon out of the ball, I'd like to study the effects of the short term."

"You want to hit two Pidgeys with one geodude?" Lyra asked.

"Precisely." Elm replied to the common term.

Walking over to the machine, she looked at each pokeball carefully. Finally choosing, she picked up the pokeball marked by the water insignia. Pressing the activation button, she unleashed the pokemon within.

"To-Totodoile!" said the small, almost crocodile-like pokemon. It smiled up at Lyra with a huge, toothy grin.

"Ah you chose Totodoile." Elm said, with a smile, "Watch out for his mouth. He'll eat _anything._ "

"Thanks for the warning, professor." Lyra said, returning the smile with one of her own, even as Totodile began doing a little dance. "But I think we'll get along pretty well."

"Why do you say that?" Asked a confused Elm.  
"Oh, no reason." Lyra replied. In truth, she had felt something almost calling to her from the ball. She felt like she had heard the chimes of faraway bells.

"Ok, then." Elm said, still slightly confused. "Oh, would you like to name your pokemon? Some trainers do."

"Maybe later. I'm not sure what to call him right now."

"Alright then. Have a safe journey."

Turning, she waved goodbye to the professor, and walked out, Totodile in tow. As soon as she was out the door however, she saw Marill and her friend Ethan.

"Oh hey, Lyra!" Ethan yelled over, before noticing Totodile, hiding behind Lyras leg. Oh, hey you got a pokemon!"

Crouching down to the hiding crocodile, Ethan held out a hand to the pokemon, a warm smile on his face.

"To-todo?" Totodile said, curious, his perpetual grin a perfect mask. Slowly making his way to the hand, he first sniffed it, tilting his head in curiosity.

Then the toothy mouth suddenly clamped down around Ethan's hand.

"Gah!" Ethan yelled out, shaking his hand wildly, trying to get the biting crocodile off.

"Totodile!" Lyra yelled, pulling on the small pokemon's jaws, trying to open them. "Ethan is my friend, don't bite him!"

Totodile suddenly let go, and for a moment Lyra and Ethan were suspended in the air, looking at each other in surprise. Then they both fell back, landing, hard.

"Owwww…" They both said, rubbing their backs.

"Sorry about him, he isn't used to being around so many humans in one day." Lyra said. "Oh, you're bleeding!"

"Nah it's fine." Ethan replied, shaking his slightly bleeding hand. "The little guy has a strong bite."

"Yeah…" Lyra said, concerned. "Are you sure you're alright?"

"Yup." Ethan said, even as Marill washed his hand with a water gun. "It'll be fine."

"Ok." Lyra said. "Well I have to go. Off to see Professor Oak."

" _The_ Professor Oak?" Ethan asked, suddenly curious.

"Yup." Lyra replied,

"Wow." Ethan sad, whistling "Put in a good word for me?"

Lyra simply smiled, rolling her eyes as she thought a single word: _Boys_.

"See ya!" Ethan said, beginning to chase his Marill. Lyra watched as he ran across the small town.

Turning to the woods she began her journey into the world of Pokemon.

…...

"How is the Operation: Azalea continuing, Tyrant?" The Rocket Executive, Archer asked, speaking to the masked, middle-sized, man crouching on a ledge. They were on one of Goldenrod City's many skyscrapers. 'Tyrant' was kneeling next to a gargoyle set on a ledge.

"The grunts have yet to be able to sneak past the woods." Tyrant replied, his voice slightly deepened by his mask, whose only design was the four arrows pointing towards the center, forming an 'X' shape. Other than that he was wearing a regular Team Rocket uniform. "They continue to tell me the reason is due to the trees and local pokemon getting in their way. I suggest sending an overseer, in order to make sure the operation is done correctly."

"Very well. I'll send Proton." Archer replied, scowling at the mention of the grunt's incompetence. "Just to make sure the operation is done flawlessly."

"He strives for perfection, too often. It can get in the way of quick results. I suggest Ariana. She is a better fighter."

"She can be too overbearing on the grunts. And she is too hot-headed for such a boring task."

"If not her then send me. At least as a reserve."

Archer thought it over for a few moments, his head tilted in thought.

"Very well. You will be there only as a reserve. Proton doesn't need to know of you. If anything goes wrong and Proton is inequipped… handle it."

"Yes, sir."

Tyrant jumped off the ledge, and Archer watched as he sent out a Pidgeotto, flying on it's back, towards Azalea Town.


	2. Chapter 2

Chapter 2: The Egg

"Lyra, wait up!" Professor Elm called out.

Lyra stopped, waiting for a breathless Professor Elm to catch up.

"Here's my pokegear number." Elm said, handing her a slip of paper.

"Oh, I don't have a pokegear." Lyra replied, as she shuffled her feet. "My mom is yet to get me one."

"I know. Your mom got you a new one as a present.." Elm said, handing her a brand new pokegear. "I already put my number and your mother's in there."

"Thank you!" Lyra said, smiling happily.

Lyra turned, and with a last wave goodbye, she walked out into the grasslands, Totodile walking next to her, his perpetual grin lightening the mood. Then they got to the tall grass. After a few steps, Totodile suddenly jumped back, right before a rattata leapt at the area he had been a second before. Lyra reacted like a pro.

"Totodile, scratch attack!" Lyra ordered. Totodile complied, running at the rattata, his small claws extended, scratching at the Rattata. After a few more scratch attacks, Totodile won out, with the rattata running away.

"Nice job!" Lyra said to the crocodile, who was puffing up his chest in pride.

They continued on through the small field, battling their way through a total of three pidgeys, four rattatas, and one spearow. Totodile learned a new move, called Rage, though Lyra didn't know what it did.

Eventually they made their way to Cherrygrove City. As soon as they walked into the town, however, an old man ran up to her with surprising speed.

"You're a rookie trainer aren't you?" the old man said, his voice blazingly fast. "I can tell! That's OK. Everyone was a rookie at one point. If you'd like I can teach you a few thing."

"Um, sure?" Lyra asked confused by her attempts to keep up with his voice.

"OK then! Follow me."

The man ran off, extremely quickly, and Lyra could barely keep up in her boots she had gotten as a present from her father. The boots were called 'igs' and were fashionable but not practicable. When he noticed her lagging behind he ran back.

"Oh, I'm sorry! I didn't notice you were wearing those boots, and not running shoes." The old man said, his tone apologetic. "I'll try to go as slow as possible."

Despite this promise he still ran from place to place, showing her the stores, a Pokemon center, the entrance to Route 30, where she was supposed to go to find Professor Oak, and the sea, along with his house.

"For your effort keeping up with me, I'll give you my running shoes." The old man said, holding out a pair of shoes. "There still warm!"

Lyra looked at the shoes with an alarmed look on her face, before looking back up at the man to see he was grinning.

"I'm kidding of course. These are brand new, don't worry."

Lyra smiled, and took the shoes, though she gave them a sniff before putting them on.

"Thank you…?" Lyra trailed off, letting the man tell her his name.

"Just call me the guide gent." the man said, before turning to leave. "Have fun!"

Lyra smiled, and ran over to the Pokemon center, testing out the new shoes. They were extremely comfortable, even without having to break them in. Entering the center she had Totodile healed by the woman at the counter.

As she headed out towards Route 30, however, the guide gent ran up to her.

"Wait!" He yelled, coming to a stop next to her. "I almost forgot something."

Quick as a meowth, he snatched up Lyra's pokegear, off of her belt and placed a chip inside. Lyra was too surprised to say anything.

"There. That's a map card." The guide gent explained, referring to the chip. "That will let you see the entire region."

"Thanks for all your help!" Lyra said, smiling at the old man.

"Of course!" The guide gent said, before turning to leave. "Travel safe.

With a last wave goodbye, Lyra walked into Route 30, walking along the path, battling wild pokemon which seemed to spring out from nowhere. Eventually she got to a house that had a fruit tree in the front. Opening the door she peeked inside the door.

"Hello? Professor Oak?" She asked, opening the door a bit more.

"Oh hello." A man said, standing up from his table. "I'm not Proffesor Oak, though many people mistake this house for his. It's farther up north."

"Oh, I'm sorry to bother you, then." Lyra said, turning to leave.

"Wait, before you go, quick question." The man said. "Do you know what apricots are?"

"What the fruit on that tree in the front?"

"Yes." The man said handing her a box. "Take this. Its an apricot case. It'll hold them and keep them fresh."

"Thank you." Lyra said, putting the box in her bag, before leaving. "Have a nice day."

Lyra made her way through the forest, going farther up north, before finally noticing another cottage. Knocking on the door, she peeked inside.

"Oh, come in!" an old man wearing a brown coat said, waving her in. "You must be Lyra."

'Yup, what do you want delivered to Professor Elm?" Lyra asked, smiling.

"Specifically, this egg." Oak said, handing her an egg about the size of her head. Taking it, it was surprisingly lighter than she had thought it would be.

Oak looked her up and down for a few moments before reaching into her pocket and pulling out a small red device.

"Take this. It's the new version of the pokedex." Oak said, handing her the small device, which Lyra pocketed.

"Thanks!" Lyra said, opening the door and leaving.

As soon as she left the cottage, however, her pokegear ringed. Activating it she heard Professor Elm's voice.

"H-hello? Lyra? It's a disaster!" Elm said, sounding scared. "Uh. Um. It's just terrible! What should I do? It… Oh no. Please get back here!"

The phone clicked, signalling him hanging up. Lyra made her way back through the forest, back to Cherrygrove, running. As she walked back towards the town, however, she heard a voice call to her.

"You got a pokemon at the lab. What a waste…"

…

Tyrant watched from the treetops as Proton sized up the giant tree in front of him. The grunts were also thinking, but of ways to get on the executive's good side.

"We need a pokemon that knows cut. Who has one?" Proton called out, his mint green hair unmoving due to how stiff it was. Much like its owner.

"None of us sir." One grunt said, after a moment.

Tyrant withrew a pokeball from his pocket, and silently sent out his scyther.

"Cut." Tyrant whispered, pointing to the tree. Almost instantly the tree was cut in half, leaving the grunts speechless, and Proton dumbfounded, though he quickly recovered.

"Don't just wait there, dolts, forward." Proton ordered.

"Yes sir!" The grunts said unanimously, though one waited behind.

"Sir was that one of your pokemon?" The grunt asked.

"Of course!" Proton lied, making Tyrant clench his fist. If Proton wasn't striving for perfection he was trying to get more credit among the grunts. A foolish endeavor, in Tyrant's opinion. Efficiency was everything. Perhaps that's why he and Archer made such a good team...


	3. Chapter 3

Chapter 3: Silver

Lyra turned around to see the owner of the voice, a boy around her age.

"Thats a pokemon too good for a wimp like you." The boy said, pulling a pokeball. Totodile growled at the boy, causing him to smirk.

"Don't you get what I'm saying?" The boy said, his smirk turning into a scowl. "Well I too have a good pokemon. I'll show you what I mean."

Chucking his pokeball, he sent out a green pokemon that looked like it had a leaf on its head. Lyra almost burst out laughing, but Totodile cocked his head in confusion.

"Chikorita, use tackle!" The boy said, and the Chikorita charged at Totodile, who took a moment before he came to his senses. Dodging out of the way, Lyra ordered Totodile to use a scratch attack.

"Scratch!"

"Tackle!"

"Rage!"

"Razor Leaf!"

As they traded moves, Totodile began to wear Chikorita down, despite its type disadvantage. As chikorita finally fell, Lyra did a small fist pump. "Nice job, Totodile!" Lyra said, hugging her partner.

"Humph! Happy you won?" The boy said with a scowl. "Do you want to know who I am?"

"Not real-"

"I'm going to be the world's greatest Pokemon Trainer."

As he finished with that he shoved past Lyra, dropping something along the way. Picking it up, Lyra noticed it was the boys trainer card. Looking, she soon found the name: Silver? What type of name was that? Noticing the card, Silver ran back and snatched it out of Lyra's hands.

"Hey, give that back! It's my trainer card!" Silver said. "Oh, no you saw my name."

As Lyra was left wondering why he cared, Silver ran down the street. Passing it off as just a man who liked his privacy, a little too much, Lyra made her way back to the town. She opened the door to Professor Elm's lab, seeing that it was a mess, and Elm was conversing with a Police officer. The officer noticed her and turned to her.

"Who are you? We are investigating the case of the missing pokemon here." The officer said, cutting off any attempt for Lyra to speak. "Rule number one! 'Whoever did it will come back to the site.' Oh my… So you must be… the one who did it?"

With that, the officer began to place handcuffs on Lyras wrist, twisting her so he faced her back.

"I'm innocent!" Lyra said, looking at the professor for help. All she saw was the stunned face that was the reaction of seeing so stupid of an officer."

"Tell it to the judge!"

Just then, Ethan burst through the door, his Marill in tow.

"Hold on a second, she has nothing to do with it!" Ethan said, almost yelling. "I saw him! A red-haired kid, looking into the building!"

"Wait red-haired?" Lyra said, thinking back to the boy. "I just battled someone like that! He had a Chikorita!"

"What? You did?" The officer said, releasing Lyra, who gripped her wrist, frowning. "He must be the one who did it! Did you get his name?"

"Yeah it was Silver."

"Silver, hm? Well thanks for helping my investigation."

With that the officer left the building. Ethan turned to Lyra.  
"Good to know they know you're innocent." He said, smiling at her, before turning to go. "See ya."

Lyra, glad that this was over, turned to Professor Elm.

"Lyra this is terrible…" Elm said, even as Lyra tried to give him the egg. Elm didn't notice it until it was directly under his nose. "Huh? This is an egg isn't it?"

"Yup, that was the package!" Lyra replied.

"This could be something I've never seen before!" Elm exclaimed. "Or it could just be a regular egg… I'll keep it for a bit to study it."

That was when Elm noticed the pokedex in Lyra's pocket.

"What? Oak gave you a pokedex?" Elm said, in surprise. "He is superb at seeing the potential in trainers! He must of had a good reason to give you one."

"Really?" Lyra said, happily surprised.

"Yes! Things are going to be fun!" Elm exclaimed. "Why don't you take Totodile with you? He seems to like you a lot."

Lyra glanced at Totodile, and the small crocodile nodded his entusiasm.

"Ok." Lyra said, looking back up at Elm.

"I suggest battling the gyms in johto." Elm said. "Maybe you can even get to the Pokemon League!"

"I'll try!" Lyra said.

With that she turned and walked out the door, ready to take on the world. But before that…

"How about I call you Sobek?" Lyra said, turning to look at Totodile. "It's after an ancient Egyptian Crocodile god."

While Totodile didn't know what Egypt was he did like the sound of the name, so he nodded enthusiastically.

"Great." Lyra said. "Welcome aboard Sobek!"

Turning she walked out into the wilderness and felt her journey had begun.

…...

Tyrant followed the group from behind as they made their way through the forest. For many people the Ilex Forest could have you lost after an hour. It was no exception for the Team Rocket group. Even after cutting the first tree, Tyrant had to go on ahead and remove at least a dozen obstacles from the forest, whether they be tree or some of the forest's stronger pokemon, as well as plant evidence that it had all been done at least a week ago, to keep them unsuspicious. Not that it would have mattered to him anyway. He just disliked leaving any loose ends to dangle.

His Scyther had proven very helpful for any and all obstacles, so he kept it out of its pokeball almost all the time. It was also a very good hunter, even for a scyther. It had been able to sniff out any hiding pokemon, and remove them from their path.

 _If they were stronger they might actually stand a chance against these pokemon,_ Tyrant though, his contempt for the grunts and Proton continuing to grow. Anything thrown at Tyrant would be blocked easily. Anything thrown at a grunt would either confuse him or simply take him out. They could be so incompetent sometimes.


	4. Chapter 4

Chapter 4: Bugs 'Sprouts and a ghost

Lyra walked along route 30, one of the empty pokeballs she had received from Ethan in her hand. She prowled the tall grass, Sobek behind her. They had yet to find a pokemon that hadn't run away, and it was getting dark. As she continued to look around, she heard some grass rustling behind her.

"Sobek, scratch!" Lyra yelled, spinning around and pointing at the bush. Sobek leapt at the bush, claws extended, scratching the grass over and over again. When he stopped, Lyra saw that there was nothing there.

"Probably just the wind." Lyra said, her smile drooping. "Lets go Sobek."

Sobek suddenly spun around and leapt at an area right next to Lyra, right before the spinarak was about to leap at Lyra.

"Sobek, use scratch!" Lyra yelled out, her smile back on at full. Maybe this was going to be her first catch.

Sobek charged the small spider-like bug, claws extended. However the spinarak was to fast, and it jumped out of the way, shooting thin bits of thread out of its mouth. Sobek was caught by the thread, and Lyra could see it slowed him down a bit. Then the spinarak shot a long stinger of purple, almost like a toothpick, at Sobek. The stinger lodged itself in Sobek's arm, and Lyra saw him cringe from the impact, but all and all, be completely fine.

"Scratch, one more time!" Lyra yelled, and this time, the spinarak was caught off guard. The attack sent the spider hurling into a tree, where it fell, its head seeming to do circles. Lyra chucked the pokeball she was holding, its activation button hitting the spinarak's torso. The bug turned into red energy, being sucked into the ball. The ball itself tilted three times, one… two… three… before finally coming to a stop, the spinarak now being caught.

Lyra picked up the ball almost reverently, seeming to treat it like a holy artifact, before pocketing it and turning to hug Sobek, who struggled to get out of her strong grip.

"WE DID IT!" Lyra yelled out, spinning in circles, Sobek gasping for air, before she noticed him, and placed him down. "Oh, sorry Sobek."

Sobek simply looked up, his grin wider than ever.

"Onward, to Violet city!" Lyra said, pointing off towards the city's shining lights in the distance.

…

Lyra got to the entrance of the city after an hour of battling with Sobek and her new friend, Spinarak. Spinarak had learned a new move, scary face, which made the opposition lose some of its will to attack quickly.

As they entered the city, Lyra was slightly disappointed by the lack of skyscrapers. Only one tower was very large and that was on the other side of town. Deciding to go to the pokemon center first she healed her pokemon, before returning outside and letting out Spinarak.

"Spin?" The small spider said, quizzically.

"Come on up here spinarak." Lyra said, holding out her hand, as the bug crawled onto her arm.

"Spina! Spinarak!" the bug said, gesturing with one of its arms towards the large tower.

"Do you want to go explore that tower?" Lyra asked, surprised by the bugs intelligence. Spinarak, in response, nodded and clacked its mandibles excitedly. Lyra smiled and walked off towards the large tower. She made good time and arrived at the front entrance in less than a minute.

"Who knows, maybe we can catch some more friends." Lyra said, to no one in particular. It was still nighttime, so the tower was lit by torches. She walked in, greeted by the sight of two giant bellsprout statues. Walking farther into the room, she also noticed three or four people, two of which looked like tourists, and the other two looked like bald monks.

"What is this place?" Lyra asked one of the monks, her expression one of awe as she looked at the large beam in the center of the room. It looked like it was waving almost.

"This is the Sprout Tower. It is built around a giant bellsprout." The man said.

Lyra looked at the monk like he was crazy, before climbing up a nearby ladder. She was greeted by the sight of another room. A second ladder was on the other side of the room, this one leading down. Crossing over there she was about two meters away, when spinarak suddenly tensed. A monk, who looked the same as the one she spoke too, came out of the darkness.

"However hard we battle…" The monk said, almost cryptically, pulling out a pokeball, "The tower will stand strong."

Throwing the ball, a plant like creature, bellsprout, she guessed, came out and attacked her spinarak, a vine coming down at the small spider. Spinarak, however, had regained its full strength and was able to escape the attack, waiting for orders from Lyra.

"Spinarak, use scary face!" Lyra ordered. The slower the opponent got, the quicker the battle would be over.

"Bellsprout, don't look!" The monk ordered, but it was too late. The bellsprout glimpsed Spinarak's back, the tattoo-like signias forming a face. The bellsprout stopped moving, its strange head suddenly one of terror.

"Now poison sting!" Lyra ordered, shooting a pin of purple poison at the plant. It hit the sprout full on, poisoning the small pokemon. The creature suddenly cringed in pain, its face turning purple, before it fainted from exhaustion.

"Very well, then." The monk said, "Go my second bellsprout."

The second bellsprout seemed to be an exact copy of the first, and was taken down just as easily. As was the third.

"I fought hard, but I'm too weak." The monk said, his face a mask of shame.

"Hey don't beat yourself up. Get stronger and I'm sure you'll beat me next time." Lyra said, comforting the monk, before walking over to the ladder.

"You are too kind." The man said, before disappearing into the darkness, even as Lyra crawled down the ladder.

As she leapt off the ladder, Lyra looked around, before noticing one area of the floor that seemed to be filled with smog. Approaching it she stuck one shoe into it, carefully. Then the smog suddenly sprang up, growing eyes and a face.

"Gastly!" the creature yelled out spitting more smog into Lyra's face.

"Gah!" Lyra yelled, coughing. "Spinarak, string shot."

Spinarak shot it's string at the creature, gastly, but it simply went straight through its body.

"What?!" Lyra said, surprised. The gastly suddenly licked Lyra's face, causing her to cringe in disgust.

"Uhh, what was that for?" Lyra asked, wiping her face.

The gastly suddenly looked extremely sad, and lonely.

"Are you lonely?" Lyra asked, curious.

The gastly turned to her and nodded, its face sad, and eyes almost watery, somehow.

"Do you want to come with me?" Lyra asked, smiling.

The gastly nodded enthusiastically, even as spinarak poked it with a leg, curiously, before seeing it pass straight through it. Lyra pulled out another empty pokeball, tapping gastly on its… face… and held the pokeball as it tilted back and forth three times, before signalling that the capture was complete. Opening the pokeball, she let out her new friend.

"So do you want to continue on up?" Lyra asked, speaking to gastly, who nodded enthusiastically.

They continued up the tower, defeating monks and wild pokemon alike. It was nearly day by the time they got to the top, and they were all very tired, but they pulled through. All of her pokemon gained levels, power and moves. Then they finally reached the last monk.

Except Red-headed Silver was already there.

"You showed us what you've got, and it is indeed good..." The elderly monk said, his voice tired. "However, you should care more about your pokemon. The way you treat your pokemon can be too harsh."

Silver scowled at the man, his face one of anger, before he turned and noticed Lyra.

"Humph! He calls himself Elder, but he was no match for me." Silver said, speaking to Lyra. "Sure enough those who lecture to be 'nice' to pokemon… They are no match for me."

"I beat you." Lyra said, simply.

"Humph! All I care about are strong pokemon. Not weaklings like you." Silver replied, before he suddenly disappeared.

Lyra walked over to the Elder and saw his expression change almost immediately.

"So good of you to come here!" The Elder said, his face one of happiness. "Sprout tower is a place where people and pokemon come to test their bonds to build a bright future together. I am the final test. Allow me to check the ties between you and your pokemon!"

Pulling out a pokeball, the Elder sent out a bellsprout that seemed slightly bigger than the ones she had previously faced.

"Gastly, use hypnosis!" Lyra ordered, having him use one of the moves he already knew.

Gastly focused on the bellsprout, and rings of purple energy came in a beam towards the plant. The bellsprout was too quick, however, and leapt out of the way, sending a group of razor sharp leaves at gastly. They struck in the area near gastly, but he also dodged.

"Lick!" Lyra ordered, having him use a not-so-friendly version of the move he had used to greet her.

The bellsprout was caught off-guard by the move and was unable to counter the attack. It cringed as Gastly's poisonous tongue came in contact with it's skin, and it fell over shivering and twitching. The Elder returned the bellsprout before sending out another.

"Nice job gastly!" Lyra said, opening its pokeball. "Return!"  
Gastly went back to its ball, and she switched him with totodile, who had also learned a new move.

"Sobek, use bite!" Lyra ordered. The totodile threw himself at the Bellsprout, his grinning mouth opened wide. The small crocodile took half of the bellsprout's body, shook him around for half a minute, before the Elder returned the plant to it's pokeball.

"Very good. You are doing well." The Elder said, before releasing his final pokemon, which, unsurprisingly, was another bellsprout.

"Sobek, bite!" Lyra said, once more.

"Bellsprout dodge!" The elder said, in response.

Sobek missed his target, slamming into the nearby beam. The bellsprout jumped to rush his attacker, growing vines to whip at the small crocodile.

He did not miss.

Lyra returned the fainted Sobek, before pulling a new pokeball from her belt.

"Go Spinarak!"

Spinarak leapt out of its ball, jumping onto the ceiling. The bellsprout's vines reached up there to get him, but the small spider was too fast for the vines. It crawled everywhere, then leapt behind Lara. As it jumped past her ear, Lyra whispered new orders to it. Then, as Spinarak was distracted, it got caught by bellsprouts vine. It was whipped up and down, making it go dizzy. Then, it was thrown back into the beam, knocking it out. Lyra returned the fainted spinarak, breathing in and then out.

"Go gastly." she said, simply dropping the ball in front of her.

"Hm. Why have you lost your will to fight." The elder asked, confused.

Lyra simply dipped her head.

"Very well." The elder said. "Bellsprout use vine whip."

Bellsprout didn't move.

"Bellsprout?" the elder asked.

Lyra suddenly burst out laughing.

"Whats so funny?" The elder asked, his face one of surprise. "What did you do?"

"String shot." Lyra simply said, smiling.

Realization dawned on the elder's face.

"Spinarak…" The elder trailed off.

"Let your bellsprout toss it around. All the while, it was throwing it's string, entrapping your bellsprout."

"But that would take a huge amount of teamwork and trust!" the elder said, incredulous. "To have gained a pokemon's trust so quickly…"

"Gastly use-"

"Bellsprout return."

Now it was Lyra's turn to be confused.

"Why did you…?" She asked, trailing off.

"It is clear you are the winner." The elder said. "My bellsprout would have lost to your gastly. Why have them go through the fight?"

Lyra smiled, and returned her own pokemon.

"How will I get over there now, though?" The elder asked, quizzically.

Realization dawned on Lyra's face.

"Oh, I'm sorry, I wasn't thinking that far ahead." she apologised, embarrassed.

"Its quite alright, my dear. I'll simply wait for my students to come and free me." The elder said, his face one of good humor. "Run along now."

"Ok, thank you for the battle!" Lyra said, making her way down to the bottom of the tower.

The elder's smile remained on his face, even as he sent out his bellsprout again.

"Razor leaf." He said, and the grass pokemon suddenly sent out a cascade of razor sharp leaves, which cut through the string, snapping each and every strand.

 _She has potential, that one,_ the elder thought, even as Lyra was walking out of the tower, towards the pokecenter, _Maybe even more than that Silver, boy._

…...

Tyrant contacted Archer, his pokegear beeping as he waited for him to pick up.

"Tyrant, what is it?" Archer asked, his voice one of serenity. Operations must have been going well.

"The Team Rocket Group led by Proton has been in the Ilex forest for some time now." Tyrant said, his frustration almost bubbling to the surface. Almost.

"How long exactly?" archer asked, his voice going dangerously low.

"Two days." Tyrant replied.

"And what should I do about it?" Archer asked, his voice one with the makings of anger.

"I need my full team." Tyrant said, his voice going low. "Not just scyther. I need Ariados, haunter, and Tyra-"

"NO." Archer said, his voice firm. "You leave to much of a mark when you have them all in one place. Make do with scyther."

"How can I get them on the move?" Tyrant asked, frustrated, but refusing to show it.

"Cut the forest down if you have to!" Archer said. "We need those slowpoke tails!"

With that Archer hanged up, and Tyrant placed his pokegear back onto his utility belt, and from behind his mask, smiled.

 _Cut the forest down if you have to._


	5. Chapter 5

Chapter 5: Bird Keepers and Rocketeers

"Use Bite!" Lyra ordered, Sobek, now a croconaw, leaping at the bird keeper's pidgey, jaws clamping down from the feathers. The small crocodile shook the bird around before releasing it when it fainted.

After the Sprout tower, Lyra had spent the night at the pokecenter, resting and training for a day. After that Lyra and her team had blown through the gym's trainers like a pile of leaves. Now all that was left was the gym leader, Falkner.

"Well done," Falkner said, approaching Lyra, "Im Falkner."

"Nice to meet you." Lyra said, nodding in greeting.

"Well, no point prolonging this." Falkner said, smiling. "Pidgey!"

Falkner tossed a single ball up in the air. Opening, it released a pidgey which dived at Sobek, its speed amazing, even for a pidgey. The crocodile was driven back by its peck.

"Water gun!" Lyra ordered, as Sobek breathed in then shot out a blast of water, forming a pillar from his mouth that followed the pidgey, before hitting it, causing it to crash onto the ground.

"Now bite!" Lyra said, taking advantage of the momentarily dazed pidgey. Sobek charged at the grounded bird pokemon, its mouth open wide. That proved to be a mistake.

"Pidgey sand-attack!" Falkner ordered.

The pidgey sent out a gust of sand, straight into Sobek's mouth, which snapped shut as the crocodile began to cough up, gasping for air with a dry mouth.

"Now tackle!" Falkner ordered, as the pidgey got back up in the air. The bird dived at Sobek, but lyra was ready.

"Now water gun!"

Sobek shot out the blast as quickly as possible, causing the pidgey to faint, but it still hit the crocodile full on, causing the croconaw to also faint.

"Sobek, return!" Lyra said, frowning. "Go gastly!"

"Go Pidgeotto!" Falkner said.

They both tossed their pokeballs at the same time. They activated at the same time, sending their contents charging at one another. Gastly enveloped pidgeotto, causing it to cringe in pain.

"Gastly, use Night Shade!" Lyra yelled, ordering gastly to use a move he had just learned. Another gastly suddenly appeared, in front of a nearby wall, a mirror image of Lyra's gastly. Pidgeotto saw this, and charged on its own accord. But the image was a fake, and pidgeotto crashed into a nearby wall, dizzy.

"Now lick!" Lyra said, and her gastly floated quickly down to pidgeotto, its tongue out as it made the large bird cringe in pain, and shiver with paralysis.

"Now, go spinarak!" Lyra said, sending out her spidery friend.

"Pidgeotto, get up!" Falkner said, trying to motivate the paralyzed bird into moving.

"Shadow Sneak, Now!"

Spinarak's shadow seemed to grow, and suddenly it was all over pidgeotto, attacking it from the left, then the right, then from behind, then the front. Pidgeotto was overwhelmed by the number and speed of the attacks, fainting.

"Pidgeotto, return." Falkner said, his smile one of resignation. "Nice job. You've earned this."

Pulling a shiny piece of metal out of his pocket he handed it to her. It was shaped like an arrow, almost.

"You will now command more respect from pokemon." Falkner said. "Well done, and good luck on your journey."

"Thank you!" Lyra said, already out the door. "See you later!"

Lyra walked out of the gym, and after healing at the pokecenter, walked to the entrance of route 32, the road to Azalea Town, home of the Azalea gym leader, a man named Bugsy, apparently. She could guess what type of pokemon he used.

Walking off to the path, she walked for Azalea, full of excitement.

…...

This is horrible timing. That thought was running through Lyra's head as she walked in the rain along the path she _thinks_ was the path to Azalea. As she walked onto a small hill she saw a figure behind her, charging up the hill. The figure knocked into her, and they both fell down, the figure falling into a mudhole.

"Who are you?" Lyra asked, after getting off the ground.

"You don't know us?" The figure, a man dressed in black, with an R emblazoned on his torso. "We are… Team Rocket!"

The figure waited a few moments as Lyra registered what she had just been told.

"You mean that group of criminals who got disbanded two years ago?" Lyra asked, her face one of doubt. The supposed Rocket member seemed surprised by her lack of fear.

"Give me a break! We have not broken up!" The man said, guffawing at the notion of her saying this. "Well, we did one time, but we had to come back to pursue Giovanni's ambition."

"Why did you just tell me your entire plan?" Lyra asked, confused.

…...

 _Why did he just tell her our entire plan?_ Tyrant thought, as he listened in on the conversation, shaking his head at the grunt's stupidity.

…

"Enough talking!" The grunt said, releasing his mistake. "Beat it!"

Shoving Lyra along, he walked back towards a nearby well, placing himself at the entrance. Lyra walked past him, and entered town, just as the rain stopped pouring. Going to the pokecenter, Lyra checked out a room for the night and slept there, letting her pokemon play among themselves.

The next day, Lyra got up and explored the town more thoroughly, and after going to the corner of the town, she saw a sign that read _Kurt's Pokeballs, Bring me Apricots, I'll make them into Pokeballs._

Lightly knocking on the door, she found it open and walked in. In the back she saw a man and a young girl. The young girl was crying, while the older man was trying to comfort her, while at the same time, trying to hold back a fit of rage.

"Hm, who are you?" The old man, Kurt, asked, noticing Lyra. "You here for some pokeballs?"

"I was wondering if you could really make apricots into-" Lyra began, but was interrupted by Kurt.

"Sorry, but that'll have to wait." Kurt said, holding up a hand. "Do you know Team Rocket?"

"Yeah, I ran into them yesterday." Lyra said, remembering the experience the previous day.

"They've been stealing and cutting off slowpoke tails for money." Kurt said, his anger bubbling over. "So I'm going to go teach them a lesson in pain!"

With that Kurt ran out the door with surprising speed, even while Lyra stood there, shocked by the old man's energy. Regaining her senses, Lyra ran after the man, trying to get to him, before he got himself hurt. She made it to the well, and saw no Kurt, or Team Rocket. Climbing down the ladder, however, she found a prone Kurt, lying on the ground.

"Hey there, lady." kurt said, holding his back. "The guard up top took off as when I shouted at him, but then I took a tumble down the well."

"Are you alright?" Lyra asked, concerned for the old man.

"I'll be fine, just go knock the hell out of those Rocket jerks!" Kurt said.

"Fine, but I'm going to-"

"Go now! The longer you wait, the more slowpokes suffer."

Accepting this, Lyra took off into the cave, quickly spotting the guard rocket. Running up to him, she looked at him with a newfound anger.

"Humph! I was standing guard up top, when some old coot started yelling at me." The Rocket said, angry at his cowardice. "He startled me so much I fell down the well."

The Rocket threw out a rattata, ready to take out his anger on Lyra.

He never stood a chance.

The same went on for another Rocket, who she blew by, as she went throughout the cave, defeating each of the Rockets. Then she arrived at the leader of them all. She laughed as soon as she saw his hair.

"What do we have here?" The man said, his smile sadistic. "I am often labeled as the scariest and cruelest guy in Team Rocket…"

…

Tyrant had to hold back a laugh to remain hidden behind the large stalagmite he was behind. That was possibly one of the dumbest things to say in a situation like this. It was hilarious.

…...

"I strongly urge you not to interfere with our business!" Proton finished.

…...

Lyra was halfway done defeating his last pokemon when Tyrant decided to make a call.

"Archer here. What is it Tyrant?" Archer asked, his voice low.

"The operation is failing due to a trainer interfering." Tyrant replied, his voice level, though quiet.

"Will Proton be able to handle it?" Archer asked, his voice exasperated.

"From the way she is beating his Golbat senseless, I would say no." Tyrant said, grimacing.

"Fine, take care of it."

…

"Spinarak, use slash!" Lyra said, her spidery friend leaping at the golbat.

"Golbat use wing attack!" Proton ordered, his voice beginning to become desperate.

"Scyther Vacuum Wave." Tyrant said, suddenly revealing himself. His scyther swept up a wind, sending trainers and pokemon tumbling alike into walls and stalagmites.

Proton was the first to recognize the newcomer.

"Tyrant?!" Proton asked, incredulous and sputtering. "What are you doing here?!"

Tyrant was silent, looking intently at Lyra, waiting to see if she got back up.

She did.  
"Sobek, use bite!" Lyra yelled, throwing out her crocodile of a pokemon, who leapt at this unknown attacker.

"Scyther use Fury cutter." Tyrant said, simply. The scyther charged right back at the leaping croconaw, claws slashing as the large bug dodged the bite.

Sobek fell onto the ground, unconscious from the severe beating.

"Alright then." Lyra said, pulling out a new pokeball. "Go Pidgeotto!"

She had caught pidgeotto the previous day, on her way to Azalea, training it from a pidgey, to a pidgeotto. She was definitely getting better. And now she had the type advantage.

"Pidgeotto, use wing attack!" Lyra ordered, and the bird charged at the scyther, it's wings glowing white.

"Scyther, use quick attack."

Suddenly scyther was below her pidgeotto, charging up at it's defenseless underbelly. Pidgeotto was forced into the ceiling, knocking it out almost instantly. Then the scyther was back at her foe's, Tyrant she believed, side.

Lyra growled. All she had left was spinarak, since she had left gastly at the pokecenter, when he stopped obeying her. Then she had an idea. Dropping spinaraks ball, she let it fall to the ground and roll off, out of sight.

"You give up?" Proton asked, almost incredulously, before regaining his composure. "Good. Now, Tyrant, end this."

Tyrant didn't move.

"Tyrant?" Proton asked. "Thats an order."

"I don't take orders from you, Proton." Tyrant replied, shocking both Proton and Lyra. "Only Archer and Giovanni."

Lyra stopped listening as Proton began arguing with a silent tyrant, even attempting to order his scyther to finish her. She only hoped that spinarak would be able to do what she hoped.

Her faith was not misplaced.

Tyrant suddenly was pulled forward, landing on the ground, hard, by an invisible force. His mask cracked and fell off, as he looked down, regaining his bearings. Scyther attempted to defend its master, taking up a protective position in front of him. Proton was confused by the sudden attack and leapt behind the scyther.

Lyra on the other hand, picked up a happy spinarak.

"Are you ready to surrender?" Lyra asked, tauntingly.

"Team Rocket does not-" Proton began.

"This operation is a failure, Proton." Tyrant said, without looking up. Without his mask, his voice sounded normal, and almost familiar to Lyra.

"What do you mean?" Proton asked, incredulous.

"She's trapped us on the other side of a wall of webs." Tyrant said, still looking at his broken mask. "We can't get to her or the slowpokes."

"Break through the webbing then!" Proton said, choosing the obvious choice.

"I can't. Neither can Scyther."

It was only then that the scyther's shaking became noticeable. The claws-for-arms then fell to the ground, fainted.

"How did-?" Proton stuttered out.

"Leech life." Tyrant replied, getting up, but still looking down, this time at his scyther. "Her spinarak has been leeching my scyther's health since the start. Well played, girl…"

Lyra's smile turned to a frown.

"Well, do you surrender?" She asked.

Tyrant was silent for a moment, before picking up pokeball off of his belt.

"Scyther return."

The fainted pokemon returned to the ball, and Tyrant walked around the webbing to the other side of the cave.

"Proton, hurry up."

Her defeated foes, grunts and the executive all ran out and up the ladder, and out of the town. Tyrant waited until the last one left, before turning to face Lyra. As soon as she saw his face, she felt a memory surface.

"Well done."

With that, Tyrant left, leaving a shocked Lyra alone in the cave. Shocked, not because she won, not because she had beaten an opponent far better than her. No.

Shocked because she knew who Tyrant was.

 _Jackson?_


End file.
